it's a design flaw in the .xm format imho, sorry. I also sometimes copy a sample, blowing up file size when I need different envelopes, tunings, panning positions and such for it. but most of the time I try to use the one copy with heavy effect command usage to get the different sounds I'd like to accomplish out of it, but sometimes I also wish for either more effect columns or copied samples in different instruments.

better don't ask about implementing it in milkytracker, as far as I've seen it tries to orient itself strictly on the fast tracker 2 .xm format, and an enhancement like that would mean breaking compatibility with that format: all other apps that can load/play/edit .xm's couldn't handle those modules. yeah, including fast tracker 2, I bet there's lots of people with original ft2 in dos-emulators or on legacy machines, and I think it's the whole point of milkytracker to stay as compatible with this as possible. not just to be able to load all the old modules from the 90's, but also to be able to put new modules on a floppy, and send it back to yourself with a time machine to a point where milkytracker did not yet exist, in order to boost your whole musical development and such...